Method for analyzing biological networks

Abstract

Significance of biological pathway in disease state is predicted by (a) providing expression level data for a plurality of biomolecules differentially expressed in a disease state, compared with same biomolecules expressed in a non-diseased state: (b) determining presence probability of the biomolecules in disease state; (c) determining effect of each biomolecule from the plurality of biomolecules on the expression of different downstream biomolecules within pathway to provide perturbation factor for each biomolecule in the pathway; (d) combining statistical significance of differentially expressed biomolecules present in the disease state, with a sum of perturbation factors for all of the biomolecules, generating an impact factor; (e) calculating statistical significance of impact factor based upon determined probability of having statistical significant presence of differentially expressed biomolecules in step (b) and the sum of perturbation factors in step (c); and (f) outputting statistical significance of impact factor for the pathway relevant to the disease.

1. A method for predicting the significance of a biological pathway in a disease state, comprising:
 (a) providing data on the expression levels of a plurality of biomolecules differentially expressed in a disease state as compared with the same biomolecules expressed in a non-disease state within said pathway: 
 (b) determining the probability of the presence of said plurality of biomolecules in said diseased state; 
 (c) determining the effect of each biomolecule from said plurality of biomolecules on the expression of different downstream biomolecules within said pathway thereby providing a perturbation factor for each biomolecule in said pathway; 
 (d) combining the statistical significance of said differentially expressed biomolecules within said pathway present in said disease state with a sum of perturbation factors for all of the biomolecules in said pathway to generate an impact factor for said pathway; 
 (e) calculating a statistical significance of said impact factor based upon a determined probability of having a statistical significant presence of differentially expressed biomolecules in step (b) and the sum of perturbation factors within said pathway in step (c); and 
 (f) outputting said statistical significance of said impact factor for said pathway relevant to said disease for a user. 
 
     
     
       2. The method of  claim 1 , wherein the biomolecule is a gene. 
     
     
       3. The method of  claim 1 , wherein the biomolecule is a mammalian metabolite.